Pairing of guanidinium moieties in water is explored by
molecular dynamics simulations of short arginine-rich peptides and ab
initio calculations of a pair of guanidinium ions in water clusters of
increasing size. Molecular dynamics simulations show that, in an aqueous
environment, the diarginine guanidinium like-charged ion pairing is
sterically hindered, whereas in the Arg-Ala-Arg tripeptide, this pairing is
significant. This result is supported by the survey of protein structure
databases, where it is found that stacked arginine pairs in
dipeptide fragments exist solely as being imposed by the protein structure.
In contrast, when two arginines are separated by a single
amino acid, their guanidinium groups can freely approach each other and
they frequently form stacked pairs. Molecular dynamics
simulations results are also supported by ab initio calculations,
which show stabilization of stacked guanidinium pairs in sufficiently
large water clusters.